Backport PR #2854 on branch 1.1.x (feat: add support for scipy 1.14.0) (

#2855) Backport PR #2854: feat: add support for scipy 1.14.0 Co-authored-by: Martin Kim <[email protected]>
scverse · Jun 26, 2024 · 93d843b · 93d843b
1 parent 7a752de
commit 93d843b
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/scvi/data/_preprocessing.py b/scvi/data/_preprocessing.py
@@ -262,7 +262,7 @@ def organize_cite_seq_10x(adata: anndata.AnnData, copy: bool = False) -> Optiona
     if copy:
         adata = adata.copy()
 
-    pro_array = adata[:, adata.var["feature_types"] == "Antibody Capture"].X.copy().A
+    pro_array = adata[:, adata.var["feature_types"] == "Antibody Capture"].X.copy().toarray()
     pro_names = np.array(adata.var_names[adata.var["feature_types"] == "Antibody Capture"])
 
     genes = (adata.var["feature_types"] != "Antibody Capture").values

diff --git a/scvi/external/scar/_model.py b/scvi/external/scar/_model.py
@@ -231,7 +231,7 @@ def get_ambient_profile(
             )
             for b in range(n_batch):
                 try:
-                    count_batch = raw_adata[batch_idx == b].X.astype(int).A
+                    count_batch = raw_adata[batch_idx == b].X.astype(int).toarray()
                 except MemoryError as err:
                     raise MemoryError("use more batches by setting a higher n_batch") from err
                 log_prob_batch = Multinomial(